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hyunhwan-jeong / SalmonTE

SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances
GNU General Public License v3.0
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Error in rule run_salmon_fq #74

Open h20gg702 opened 1 year ago

h20gg702 commented 1 year ago

Hi, I am trying to use SalmonTE.py quant --reference=hs example, but I faced a problem like below. Could you suggest a solution? I tried brew install tbb, but I still have. `SalmonTE.py quant --reference=hs example 2023-05-09 19:37:29,530 Starting quantification mode 2023-05-09 19:37:29,530 Collecting FASTQ files... 2023-05-09 19:37:29,530 SalmonTE assumes that 'example' is a directory, and SalmonTE will search any FASTQ file in the directory. 2023-05-09 19:37:29,539 The input dataset is considered as a paired-ends dataset. 2023-05-09 19:37:29,540 Collected 4 FASTQ files. 2023-05-09 19:37:29,540 Quantification has been finished. 2023-05-09 19:37:29,540 Running Salmon using Snakemake Building DAG of jobs... 2023-05-09 19:37:30,474 Building DAG of jobs... Using shell: /bin/bash 2023-05-09 19:37:30,514 Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) 2023-05-09 19:37:30,514 Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. 2023-05-09 19:37:30,514 Rules claiming more threads will be scaled down. Job stats: job count min threads max threads

all 1 1 1 collect_abundance 1 1 1 collect_mappability 1 1 1 run_salmon_fq 4 1 1 total 7 1 1

2023-05-09 19:37:30,521 Job stats: job count min threads max threads

all 1 1 1 collect_abundance 1 1 1 collect_mappability 1 1 1 run_salmon_fq 4 1 1 total 7 1 1

Select jobs to execute... 2023-05-09 19:37:30,521 Select jobs to execute... /bin/bash: line 1: 12314 Abort trap: 6 /Users/yoshiakisato/SalmonTE/salmon/darwin/bin/salmon quant -q -i /Users/yoshiakisato/SalmonTE/reference/hs -l A -1 /var/folders/pv/zvpnvfk901qdw74sqzy8vg7r0000gn/T/tmpekehwfec/CTRL_2_R1.fastq -2 /var/folders/pv/zvpnvfk901qdw74sqzy8vg7r0000gn/T/tmpekehwfec/CTRL_2_R2.fastq -o /Users/yoshiakisato/SalmonTE/SalmonTE_output/CTRL_2 -p 4 2> /dev/null [Tue May 9 19:37:30 2023] 2023-05-09 19:37:30,745 [Tue May 9 19:37:30 2023] Error in rule run_salmon_fq: jobid: 4 input: /Users/yoshiakisato/SalmonTE/reference/hs, /var/folders/pv/zvpnvfk901qdw74sqzy8vg7r0000gn/T/tmpekehwfec/CTRL_2_R1.fastq, /var/folders/pv/zvpnvfk901qdw74sqzy8vg7r0000gn/T/tmpekehwfec/CTRL_2_R2.fastq output: /Users/yoshiakisato/SalmonTE/SalmonTE_output/CTRL_2 shell: /Users/yoshiakisato/SalmonTE/salmon/darwin/bin/salmon quant -q -i /Users/yoshiakisato/SalmonTE/reference/hs -l A -1 /var/folders/pv/zvpnvfk901qdw74sqzy8vg7r0000gn/T/tmpekehwfec/CTRL_2_R1.fastq -2 /var/folders/pv/zvpnvfk901qdw74sqzy8vg7r0000gn/T/tmpekehwfec/CTRL_2_R2.fastq -o /Users/yoshiakisato/SalmonTE/SalmonTE_output/CTRL_2 -p 4 2>/dev/null (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

2023-05-09 19:37:30,745 Error in rule run_salmon_fq: jobid: 4 input: /Users/yoshiakisato/SalmonTE/reference/hs, /var/folders/pv/zvpnvfk901qdw74sqzy8vg7r0000gn/T/tmpekehwfec/CTRL_2_R1.fastq, /var/folders/pv/zvpnvfk901qdw74sqzy8vg7r0000gn/T/tmpekehwfec/CTRL_2_R2.fastq output: /Users/yoshiakisato/SalmonTE/SalmonTE_output/CTRL_2 shell: /Users/yoshiakisato/SalmonTE/salmon/darwin/bin/salmon quant -q -i /Users/yoshiakisato/SalmonTE/reference/hs -l A -1 /var/folders/pv/zvpnvfk901qdw74sqzy8vg7r0000gn/T/tmpekehwfec/CTRL_2_R1.fastq -2 /var/folders/pv/zvpnvfk901qdw74sqzy8vg7r0000gn/T/tmpekehwfec/CTRL_2_R2.fastq -o /Users/yoshiakisato/SalmonTE/SalmonTE_output/CTRL_2 -p 4 2>/dev/null (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time. 2023-05-09 19:37:30,746 Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message 2023-05-09 19:37:30,747 Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2023-05-09T193729.706500.snakemake.log 2023-05-09 19:37:30,747 Complete log: .snakemake/log/2023-05-09T193729.706500.snakemake.log Traceback (most recent call last): File "/Users/yoshiakisato/SalmonTE/SalmonTE.py", line 293, in run(args) File "/Users/yoshiakisato/SalmonTE/SalmonTE.py", line 244, in run run_salmon(param) File "/Users/yoshiakisato/SalmonTE/SalmonTE.py", line 157, in run_salmon with open(os.path.join(param["--outpath"], "EXPR.csv" ), "r") as inp: FileNotFoundError: [Errno 2] No such file or directory: '/Users/yoshiakisato/SalmonTE/SalmonTE_output/EXPR.csv'`

hyunhwan-jeong commented 1 year ago

Hi @h20gg702, I guess it is related to #75, and could you tell me that what version of snakemake you are using?

h20gg702 commented 1 year ago

Dear hyunhwan-jeong, 

snakemake --version
7.25.3

Thanks.

h20gg702 commented 11 months ago

Hi hyunhwan-jeong, when I used the command appeared in error message like following ./salmon/darwin/bin/salmon quant -q -i reference/hs -l A -1 /var/folders/pv/zvpnvfk901qdw74sqzy8vg7r0000gn/T/tmpr25su1_l/CTRL_2_R1.fastq -2 /var/folders/pv/zvpnvfk901qdw74sqzy8vg7r0000gn/T/tmpr25su1_l/CTRL_2_R2.fastq -o /Users/yoshiakisato/SalmonTE/SalmonTE_output/CTRL_2, I got this message. `Version Info: ### PLEASE UPGRADE SALMON ###

A newer version of salmon with important bug fixes and improvements is available.

The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience.

Sign up for the salmon mailing list to hear about new versions, features and updates at: https://oceangenomics.com/subscribe

` and I got CTRL_2 folder in Salmon_output directory. So I repeated using the salmon quant for CTRL_1, TARDBP_1, and TARDBP_2 like CTRL_2, and finally I got following message after ./SalmonTE.py quant --reference=hs example

`2023-07-20 13:12:32,712 Starting quantification mode 2023-07-20 13:12:32,712 Collecting FASTQ files... 2023-07-20 13:12:32,712 SalmonTE assumes that 'example' is a directory, and SalmonTE will search any FASTQ file in the directory. 2023-07-20 13:12:32,721 The input dataset is considered as a paired-ends dataset. 2023-07-20 13:12:32,721 Collected 4 FASTQ files. 2023-07-20 13:12:32,721 Quantification has been finished. 2023-07-20 13:12:32,721 Running Salmon using Snakemake Building DAG of jobs... 2023-07-20 13:12:33,511 Building DAG of jobs... Using shell: /bin/bash 2023-07-20 13:12:33,547 Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) 2023-07-20 13:12:33,547 Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. 2023-07-20 13:12:33,547 Rules claiming more threads will be scaled down. Job stats: job count min threads max threads

all 1 1 1 collect_abundance 1 1 1 collect_mappability 1 1 1 total 3 1 1

2023-07-20 13:12:33,553 Job stats: job count min threads max threads

all 1 1 1 collect_abundance 1 1 1 collect_mappability 1 1 1 total 3 1 1

Select jobs to execute... 2023-07-20 13:12:33,553 Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Select jobs to execute... Select jobs to execute... 2023-07-20 13:12:34,993 Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Select jobs to execute... Select jobs to execute... 2023-07-20 13:12:36,078 Select jobs to execute... Complete log: .snakemake/log/2023-07-20T131232.940840.snakemake.log 2023-07-20 13:12:36,079 Complete log: .snakemake/log/2023-07-20T131232.940840.snakemake.log` and in SalmonTE_output directory, EXPR.csv, MAPPING_INFO.csv, clades.csv, condition.csv files are appeared. but salmon_quant.log has empty contents. Does this result of salmon quant has anything wrong?